Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: evidence from Raman markers assignments
Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: evidence from Raman markers assignments
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DOI：
10.1093/nar/27.5.1398
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发表时间：
1999-03-01
影响因子：
14.9
通讯作者：
Ghomi, M
中科院分区：
文献类型：
--
作者：
Leulliot, N;Baumruk, V;Ghomi, M
UNCG和GNRA四环（其中N是四种核苷酸中的任何一种，R是嘌呤）的高分辨率NMR数据表明，除了RNA链中经常遇到的3 '-内/反构象外，它们还含有具有不寻常的2'-内/反和3 '-内/顺构象的核糖核苷。在当前的研究中，拉曼光谱已用于探测这些核苷构象，并在5-80摄氏度温度范围内遵循水相中的有序（发夹）到无序（随机链）结构转变。GCAA和GAAA四环的光谱演化，形成在非常短的发夹中，只有三个G。C碱基对（T-m > 60 ℃），并与UUCG和UACG四环上发表的结果进行了比较，后者的末端鸟嘌呤的顺式取向以及第三个rC残基的2 ′-内/反式构象已通过振动标记带得到证实，作为温度的函数获得的拉曼数据表明，UUCG四环中的第一个尿嘧啶是堆叠的，而中间的两个残基是堆叠的。（rU和rC）处于2 '-内/反构象，与先前公布的NMR结果一致。就有关GNRA型四环的新数据而言，它们使我们得出结论：（一）在两种情况下（ii）GCAA四环中的第二个rC残基具有3 ′-内/反构象;（iii）如NMR结果所预测的，与两个四环中的第三个rA残基相关的糖皱褶可能经历3 ′-内/2 ′-内相互转化;（iv）茎采用规则的A-型结构;（v）这两个GNRA四环的所有其他核苷具有通常的3 '-内/反构象。
High resolution NMR data on UNCG and GNRA tetraloops (where N is any of the four nucleotides and R is a purine) have shown that they contain ribonucleosides with unusual 2'-endo/anti and 3'-endo/syn conformations, in addition to the 3'-endo/anti ones which are regularly encountered in RNA chains. in the current study, Raman spectroscopy has been used to probe these nucleoside conformations and follow the order (hairpin) to disorder (random chain) structural transitions in aqueous phase in the 5-80 degrees C temperature range. Spectral evolution of GCAA and GAAA tetraloops, as formed in very short hairpins with only three G . C base pairs in their stems (T-m > 60 degrees C), are reported and compared with those previously published on UUCG and UACG tetraloops, for which the syn orientation of the terminal guanine as well as the 2'-endo/anti conformation of the third rC residue have been confirmed by means of vibrational marker bands, Raman data obtained as a function of temperature show that the first uracil in the UUCG tetraloop is stacked and the two middle residues (rU and rC) are in the 2'-endo/anti conformation, in agreement with the previously published NMR results, As far as the new data concerning the GNRA type tetraloops are concerned, they lead us to conclude that: (i) in both cases (GCAA and GAAA tetraloops) the adenine bases are stacked; (ii) the second rC residue in the GCAA tetraloop has a 3'-endo/anti conformation; (iii) the sugar pucker associated with the third rA residue in both tetraloops possibly undergoes a 3'-endo/2'-endo interconversion as predicted by NMR results; (iv) the stem adopts a regular A-form structure; (v) all other nucleosides of these two GNRA tetraloops possess the usual 3'-endo/anti conformation.